Contacts of the helix formed by residues 137 - 145 (chain A) in PDB entry 3LUE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 137 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 4.3 5.9 - - - +
12A ASN 4.0 17.9 + - - -
13A GLY* 5.9 2.0 - - - -
74A GLY* 5.1 4.0 + - - -
106A THR* 3.8 13.1 + - - +
107A GLU* 3.0 34.9 + - - +
108A ALA* 3.3 10.5 - - - +
109A PRO* 4.7 1.5 - - - +
136A ILE* 1.3 73.2 - - - +
138A ALA* 1.4 62.2 + - - +
140A LEU* 3.2 15.0 + - - +
141A SER 3.3 8.8 + - - -
154A ASP* 2.9 10.4 - - - +
156A GLY* 4.0 21.5 - - - -
157A ASP 5.0 2.5 + - - +
339A VAL* 3.4 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 4.8 0.4 - - + -
136A ILE* 3.5 8.8 - - + +
137A GLN* 1.4 70.3 - - - +
139A VAL* 1.3 63.0 + - - +
141A SER* 3.3 5.0 + - - -
142A LEU* 3.1 18.2 + - - +
152A VAL* 3.5 15.1 - - + +
154A ASP* 1.5 66.3 + - + +
161A HIS* 4.7 3.4 - - + +
163A VAL* 5.0 7.6 - - + -
300A SER* 3.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA* 6.1 1.1 - - + -
136A ILE* 3.5 25.2 + - + +
137A GLN 3.3 0.8 - - - -
138A ALA* 1.3 77.9 - - - +
140A LEU* 1.3 59.5 + - + +
142A LEU* 3.5 8.1 + - - +
143A TYR* 3.3 25.9 + - + +
163A VAL* 3.6 38.8 - - + -
165A ILE* 5.3 3.1 - - + -
170A ALA* 4.8 7.2 - - + -
375A PHE* 4.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 5.2 0.4 - - + -
104A LEU* 3.9 6.3 - - + -
106A THR* 3.3 30.5 - - + -
135A ALA* 3.4 21.3 - - + -
136A ILE 2.9 30.3 - - - +
137A GLN 3.2 5.1 + - - +
139A VAL* 1.3 77.2 - - + +
141A SER* 1.3 66.2 + - - +
142A LEU 3.3 0.2 - - - -
143A TYR* 4.5 4.3 - - - +
144A ALA* 3.1 19.4 + - - +
338A SER 4.2 1.1 - - - -
339A VAL* 3.3 24.5 - - + +
342A GLY* 3.1 14.7 - - - +
343A GLY* 3.6 27.6 - - - +
346A LEU* 5.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLN 3.3 2.2 + - - -
138A ALA 3.3 5.4 + - - -
140A LEU* 1.3 80.0 - - - +
142A LEU* 1.3 59.8 + - - -
144A ALA* 3.5 3.5 + - - +
145A SER* 3.4 18.7 + - - -
152A VAL* 4.4 2.5 - - - -
154A ASP* 3.4 1.6 + - - -
298A VAL* 6.0 4.2 - - - +
300A SER* 2.8 41.2 + - - -
338A SER* 3.6 22.3 + - - -
339A VAL* 3.2 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA 3.1 5.5 + - - +
139A VAL 3.6 8.3 - - - +
140A LEU 3.3 0.2 - - - -
141A SER* 1.3 75.3 - - - +
143A TYR* 1.3 66.7 + - - +
145A SER* 2.8 30.8 + - - +
147A ARG* 3.9 12.9 - - + +
148A THR 6.3 1.1 - - - -
149A THR 5.9 1.1 - - - +
150A GLY* 5.0 4.0 - - - +
151A ILE 4.6 6.3 - - - +
152A VAL* 2.1 45.2 - - + +
165A ILE* 1.5 72.5 - - + -
298A VAL* 4.6 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.3 14.6 + - + +
140A LEU* 4.1 6.7 - - - +
142A LEU* 1.3 79.1 - - - +
144A ALA* 1.3 62.6 + - - +
145A SER 3.2 5.7 + - - -
147A ARG 4.9 1.5 - - - +
168A GLY* 4.5 23.8 - - - -
342A GLY 4.6 7.9 - - - +
345A ILE* 4.0 32.4 - - + +
346A LEU* 4.7 20.0 - - + -
349A LEU* 4.0 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU 3.1 20.0 + - - +
141A SER* 3.8 5.2 - - - +
142A LEU 3.2 0.4 - - - -
143A TYR* 1.3 76.1 - - - +
145A SER* 1.3 57.5 + - - +
146A GLY 4.6 0.2 + - - -
338A SER* 4.1 10.1 - - - +
341A ILE* 4.0 9.6 - - + +
342A GLY* 3.4 22.3 - - - +
345A ILE* 4.0 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER 3.4 9.0 + - - -
142A LEU* 2.8 33.0 + - - +
143A TYR 4.0 3.8 - - - -
144A ALA* 1.3 78.7 - - - +
146A GLY* 1.3 61.4 + - - +
147A ARG* 1.9 36.8 + - - +
298A VAL* 5.2 10.3 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il